4Y06
 
 | | Crystal structure of the DAP BII (G675R) dipeptide complex | | 分子名称: | Dipeptidyl aminopeptidase BII, GLUTAMIC ACID, GLYCEROL, ... | | 著者 | Sakamoto, Y, Iizuka, I, Tateoka, C, Roppongi, S, Fujimoto, M, Nonaka, T, Ogasawara, W, Tanaka, N. | | 登録日 | 2015-02-05 | | 公開日 | 2015-07-15 | | 最終更新日 | 2024-11-06 | | 実験手法 | X-RAY DIFFRACTION (2.18 Å) | | 主引用文献 | Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Sci Rep, 5, 2015
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3B1C
 | | Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form | | 分子名称: | BetaC-S lyase, GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, ... | | 著者 | Kezuka, Y, Yoshida, Y, Nonaka, T. | | 登録日 | 2011-06-29 | | 公開日 | 2012-06-27 | | 最終更新日 | 2025-03-26 | | 実験手法 | X-RAY DIFFRACTION (1.93 Å) | | 主引用文献 | Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80, 2012
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3B1E
 | | Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate form | | 分子名称: | 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ACETATE ION, ... | | 著者 | Kezuka, Y, Yoshida, Y, Nonaka, T. | | 登録日 | 2011-06-29 | | 公開日 | 2012-06-27 | | 最終更新日 | 2024-10-16 | | 実験手法 | X-RAY DIFFRACTION (1.78 Å) | | 主引用文献 | Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80, 2012
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7DKD
 | | Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr | | 分子名称: | ASPARAGINE, Dipeptidyl-peptidase, GLYCEROL, ... | | 著者 | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | 登録日 | 2020-11-23 | | 公開日 | 2021-11-03 | | 最終更新日 | 2024-11-13 | | 実験手法 | X-RAY DIFFRACTION (1.92 Å) | | 主引用文献 | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKC
 | | Stenotrophomonas maltophilia DPP7 in complex with Tyr-Tyr | | 分子名称: | Dipeptidyl-peptidase, GLYCEROL, TYROSINE | | 著者 | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | 登録日 | 2020-11-23 | | 公開日 | 2021-11-03 | | 最終更新日 | 2024-11-06 | | 実験手法 | X-RAY DIFFRACTION (1.86 Å) | | 主引用文献 | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKE
 | | Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr | | 分子名称: | Dipeptidyl-peptidase, GLYCEROL, PHENYLALANINE, ... | | 著者 | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | 登録日 | 2020-11-23 | | 公開日 | 2021-11-03 | | 最終更新日 | 2024-11-06 | | 実験手法 | X-RAY DIFFRACTION (1.91 Å) | | 主引用文献 | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKB
 | | Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr | | 分子名称: | Dipeptidyl-peptidase, TYROSINE, VALINE | | 著者 | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | 登録日 | 2020-11-23 | | 公開日 | 2021-11-03 | | 最終更新日 | 2024-11-06 | | 実験手法 | X-RAY DIFFRACTION (2.03 Å) | | 主引用文献 | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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2Y0F
 | | STRUCTURE OF GCPE (IspG) FROM THERMUS THERMOPHILUS HB27 | | 分子名称: | 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE, IRON/SULFUR CLUSTER | | 著者 | Rekittke, I, Nonaka, T, Wiesner, J, Demmer, U, Warkentin, E, Jomaa, H, Ermler, U. | | 登録日 | 2010-12-02 | | 公開日 | 2011-01-26 | | 最終更新日 | 2024-05-08 | | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | | 主引用文献 | Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Synthase (Gcpe) from Thermus Thermophilus.
FEBS Lett., 585, 2011
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1JVS
 | | Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase; a target enzyme for antimalarial drugs | | 分子名称: | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION | | 著者 | Yajima, S, Nonaka, T, Kuzuyama, T, Seto, H, Ohsawa, K. | | 登録日 | 2001-08-31 | | 公開日 | 2002-10-09 | | 最終更新日 | 2024-10-30 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with cofactors: implications of a flexible loop movement upon substrate binding.
J.Biochem., 131, 2002
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5Z5C
 | | Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form | | 分子名称: | CHLORIDE ION, Cysteine synthase, PYRIDOXAL-5'-PHOSPHATE | | 著者 | Kezuka, Y, Yoshida, Y, Nonaka, T. | | 登録日 | 2018-01-17 | | 公開日 | 2018-02-14 | | 最終更新日 | 2025-04-09 | | 実験手法 | X-RAY DIFFRACTION (2.07 Å) | | 主引用文献 | Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,
Biochem. J., 475, 2018
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6IOY
 | | Crystal structure of Porphyromonas gingivalis acetate kinase | | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, Acetate kinase, SULFATE ION | | 著者 | Kezuka, Y, Yoshida, Y, Nonaka, T. | | 登録日 | 2018-10-31 | | 公開日 | 2019-04-24 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.94 Å) | | 主引用文献 | Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis.
J Oral Microbiol, 11, 2019
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2DBT
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6IOW
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6IOX
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2D49
 | | Solution structure of the Chitin-Binding Domain of Streptomyces griseus Chitinase C | | 分子名称: | chitinase C | | 著者 | Akagi, K, Watanabe, J, Hara, M, Kezuka, Y, Chikaishi, E, Yamaguchi, T, Akutsu, H, Nonaka, T, Watanabe, T, Ikegami, T. | | 登録日 | 2005-10-11 | | 公開日 | 2006-10-11 | | 最終更新日 | 2024-10-23 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Identification of the substrate interaction region of the chitin-binding domain of Streptomyces griseus chitinase C
J.Biochem.(Tokyo), 139, 2006
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2DKC
 | | Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the substrate complex | | 分子名称: | 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose, PHOSPHATE ION, Phosphoacetylglucosamine mutase, ... | | 著者 | Nishitani, Y, Maruyama, D, Nonaka, T, Kita, A, Fukami, T.A, Mio, T, Yamada-Okabe, H, Yamada-Okabe, T, Miki, K. | | 登録日 | 2006-04-07 | | 公開日 | 2006-05-16 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Crystal Structures of N-Acetylglucosamine-phosphate Mutase, a Member of the {alpha}-D-Phosphohexomutase Superfamily, and Its Substrate and Product Complexes.
J.Biol.Chem., 281, 2006
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5YP4
 | | Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pro from Pseudoxanthomonas mexicana WO24 | | 分子名称: | Dipeptidyl aminopeptidase 4, GLYCEROL, LYSINE, ... | | 著者 | Roppongi, S, Suzuki, Y, Tateoka, C, Fuimoto, M, Morisawa, S, Iizuka, I, Nakamura, A, Honma, N, Shida, Y, Ogasawara, W, Tanaka, N, Sakamoto, Y, Nonaka, T. | | 登録日 | 2017-11-01 | | 公開日 | 2018-02-21 | | 最終更新日 | 2024-11-13 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Sci Rep, 8, 2018
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5YP1
 | | Crystal structure of dipeptidyl peptidase IV (DPP IV) from Pseudoxanthomonas mexicana WO24 | | 分子名称: | Dipeptidyl aminopeptidase 4, GLYCEROL | | 著者 | Roppongi, S, Suzuki, Y, Tateoka, C, Fuimoto, M, Morisawa, S, Iizuka, I, Nakamura, A, Honma, N, Shida, Y, Ogasawara, W, Tanaka, N, Sakamoto, Y, Nonaka, T. | | 登録日 | 2017-11-01 | | 公開日 | 2018-02-21 | | 最終更新日 | 2024-11-13 | | 実験手法 | X-RAY DIFFRACTION (2.47 Å) | | 主引用文献 | Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Sci Rep, 8, 2018
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2DKD
 | | Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the product complex | | 分子名称: | 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-galactopyranose, PHOSPHATE ION, Phosphoacetylglucosamine mutase, ... | | 著者 | Nishitani, Y, Maruyama, D, Nonaka, T, Kita, A, Fukami, T.A, Mio, T, Yamada-Okabe, H, Yamada-Okabe, T, Miki, K. | | 登録日 | 2006-04-07 | | 公開日 | 2006-05-16 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Crystal Structures of N-Acetylglucosamine-phosphate Mutase, a Member of the {alpha}-D-Phosphohexomutase Superfamily, and Its Substrate and Product Complexes.
J.Biol.Chem., 281, 2006
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5YP2
 | | Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24 | | 分子名称: | (2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile, Dipeptidyl aminopeptidase 4, GLYCEROL | | 著者 | Roppongi, S, Suzuki, Y, Tateoka, C, Fuimoto, M, Morisawa, S, Iizuka, I, Nakamura, A, Honma, N, Shida, Y, Ogasawara, W, Tanaka, N, Sakamoto, Y, Nonaka, T. | | 登録日 | 2017-11-01 | | 公開日 | 2018-02-21 | | 最終更新日 | 2024-11-13 | | 実験手法 | X-RAY DIFFRACTION (2.13 Å) | | 主引用文献 | Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Sci Rep, 8, 2018
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5YP3
 | | Crystal structure of dipeptidyl peptidase IV (DPP IV) with Ile-Pro from Pseudoxanthomonas mexicana | | 分子名称: | Dipeptidyl aminopeptidase 4, GLYCEROL, ISOLEUCINE, ... | | 著者 | Roppongi, S, Suzuki, Y, Tateoka, C, Fuimoto, M, Morisawa, S, Iizuka, I, Nakamura, A, Honma, N, Shida, Y, Ogasawara, W, Tanaka, N, Sakamoto, Y, Nonaka, T. | | 登録日 | 2017-11-01 | | 公開日 | 2018-02-21 | | 最終更新日 | 2024-10-30 | | 実験手法 | X-RAY DIFFRACTION (2.44 Å) | | 主引用文献 | Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Sci Rep, 8, 2018
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1IO5
 | | HYDROGEN AND HYDRATION OF HEN EGG-WHITE LYSOZYME DETERMINED BY NEUTRON DIFFRACTION | | 分子名称: | LYSOZYME C | | 著者 | Niimura, N, Minezaki, Y, Nonaka, T, Castagna, J.C, Cipriani, F, Hoeghoej, P, Lehmann, M.S, Wilkinson, C. | | 登録日 | 2001-01-14 | | 公開日 | 2001-02-07 | | 最終更新日 | 2024-10-16 | | 実験手法 | NEUTRON DIFFRACTION (2 Å) | | 主引用文献 | Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.
Nat.Struct.Biol., 4, 1997
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2DKA
 | | Crystal structure of N-acetylglucosamine-phosphate mutase, a member of the alpha-D-phosphohexomutase superfamily, in the apo-form | | 分子名称: | Phosphoacetylglucosamine mutase | | 著者 | Nishitani, Y, Maruyama, D, Nonaka, T, Kita, A, Fukami, T.A, Mio, T, Yamada-Okabe, H, Yamada-Okabe, T, Miki, K. | | 登録日 | 2006-04-07 | | 公開日 | 2006-05-16 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.93 Å) | | 主引用文献 | Crystal Structures of N-Acetylglucosamine-phosphate Mutase, a Member of the {alpha}-D-Phosphohexomutase Superfamily, and Its Substrate and Product Complexes.
J.Biol.Chem., 281, 2006
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2DFX
 | | Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor | | 分子名称: | Colicin-E5, Colicin-E5 immunity protein | | 著者 | Yajima, S, Inoue, S, Ogawa, T, Nonaka, T, Ohsawa, K, Masaki, H. | | 登録日 | 2006-03-06 | | 公開日 | 2007-01-23 | | 最終更新日 | 2025-04-30 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction
Nucleic Acids Res., 34, 2006
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2DJH
 | | Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 | | 分子名称: | 2'-DEOXYURIDINE 3'-MONOPHOSPHATE, 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE, Colicin-E5 | | 著者 | Yajima, S, Inoue, S, Ogawa, T, Nonaka, T, Ohsawa, K, Masaki, H. | | 登録日 | 2006-04-03 | | 公開日 | 2007-01-23 | | 最終更新日 | 2023-10-25 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction
Nucleic Acids Res., 34, 2006
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